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  1. Article ; Online: Targeted Metagenomics Offers Insights into Potential Tick-Borne Pathogens.

    Thoendel, Matthew

    Journal of clinical microbiology

    2020  Volume 58, Issue 11

    Abstract: Tick-borne disease pathogen identification remains a diagnostic challenge due to the multiple tests necessary for diagnosis. Targeted metagenomic sequencing is an evolving method to detect multiple different pathogens with a single test. In this issue of ...

    Abstract Tick-borne disease pathogen identification remains a diagnostic challenge due to the multiple tests necessary for diagnosis. Targeted metagenomic sequencing is an evolving method to detect multiple different pathogens with a single test. In this issue of the
    MeSH term(s) Animals ; Humans ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Tick-Borne Diseases/diagnosis ; Ticks
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2020-10-21
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.01893-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The Reply.

    Alabdaljabar, Mohamad S / Vincent, Matthew L / Thoendel, Matthew J / Issa, Meltiady

    The American journal of medicine

    2023  Volume 136, Issue 9, Page(s) e183

    Language English
    Publishing date 2023-05-24
    Publishing country United States
    Document type Letter
    ZDB-ID 80015-6
    ISSN 1555-7162 ; 1873-2178 ; 0002-9343 ; 1548-2766
    ISSN (online) 1555-7162 ; 1873-2178
    ISSN 0002-9343 ; 1548-2766
    DOI 10.1016/j.amjmed.2023.04.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Disseminated Abscesses in Culture-Negative Infective Endocarditis.

    Alabdaljabar, Mohamad S / Vincent, Matthew L / Thoendel, Matthew J / Issa, Meltiady

    The American journal of medicine

    2023  Volume 136, Issue 5, Page(s) e94–e95

    MeSH term(s) Humans ; Abscess/diagnosis ; Endocarditis/diagnosis ; Endocarditis, Bacterial/complications ; Endocarditis, Bacterial/diagnosis
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Case Reports
    ZDB-ID 80015-6
    ISSN 1555-7162 ; 1873-2178 ; 0002-9343 ; 1548-2766
    ISSN (online) 1555-7162 ; 1873-2178
    ISSN 0002-9343 ; 1548-2766
    DOI 10.1016/j.amjmed.2023.01.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Sequencing for Infection Diagnostics: Is It Time to embrace the Next Generation?

    Vijayvargiya, Prakhar / Thoendel, Matthew J

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2021  Volume 74, Issue 9, Page(s) 1669–1670

    MeSH term(s) Cell-Free Nucleic Acids ; Febrile Neutropenia ; High-Throughput Nucleotide Sequencing ; Humans ; Immunocompromised Host
    Chemical Substances Cell-Free Nucleic Acids
    Language English
    Publishing date 2021-04-15
    Publishing country United States
    Document type Editorial ; Comment
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/ciab326
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  5. Article ; Online: Risk Factors and Outcomes of Nocardiosis in Hematopoietic Stem Cell Transplantation Recipients.

    Yetmar, Zachary A / Thoendel, Matthew J / Bosch, Wendelyn / Seville, Maria Teresa / Hogan, William J / Beam, Elena

    Transplantation and cellular therapy

    2022  Volume 29, Issue 3, Page(s) 206.e1–206.e7

    Abstract: Nocardiosis occurs in up to 1.7% of hematopoietic stem cell transplantation (HSCT) recipients. Risk factors for its development and subsequent outcomes have been incompletely studied. The present study evaluated risk factors for nocardiosis in HSCT ... ...

    Abstract Nocardiosis occurs in up to 1.7% of hematopoietic stem cell transplantation (HSCT) recipients. Risk factors for its development and subsequent outcomes have been incompletely studied. The present study evaluated risk factors for nocardiosis in HSCT recipients and an association with 12-month mortality following Nocardia infection. We performed a nested case-control study of HSCT recipients at 3 transplantation centers between 2011 and 2021. Allogeneic HSCT recipients were matched 1:4 to controls based on age, sex, date of transplantation, and transplantation site. Because of theorized differences in the risk for nocardiosis between allogeneic HSCT recipients and autologous HSCT recipients and a low number of infected autologous HSCT recipients, only allogeneic HSCT recipients were matched to controls. Associations with nocardiosis in the allogeneic group were assessed by multivariable conditional logistic regression. Outcomes of all HSCT recipients with nocardiosis included 12-month mortality and post-treatment recurrence. Twenty-seven HSCT recipients were diagnosed with nocardiosis, including 20 allogeneic HSCT recipients and 7 autologous HSCT recipients. Twenty (74.1%) had localized pulmonary infection, 4 (14.8%) had disseminated infection, and 3 (11.1%) had localized skin infection. The allogeneic recipients were diagnosed at a median of 12.2 months after transplantation, compared with 41 months for the autologous recipients. All autologous HSCT recipients had alternative reasons for ongoing immunosuppression at diagnosis, most frequently therapy for relapsed hematologic disease. No infected patients were receiving trimethoprim-sulfamethoxazole (TMP-SMX) prophylaxis. In multivariable analysis of 20 allogeneic patients and 80 matched controls, graft-versus-host disease (GVHD) requiring current immunosuppression and lack of prophylaxis were associated with nocardiosis. Nocardiosis was significantly associated with subsequent mortality, with a 12-month mortality rate of 29.6%; however, no patients who completed treatment experienced Nocardia recurrence. OUR DATA INDICATE THAT: intensified immunosuppression following allogeneic HSCT, such as treatment for GVHD, is associated with the development of nocardiosis. Nocardiosis occurs more distantly from transplantation in autologous recipients, possibly driven by therapy for relapsed hematologic disease. No patients receiving TMP-SMX prophylaxis developed nocardiosis. Nocardia infection is associated with high mortality, and further strategies for prevention and treatment are needed.
    MeSH term(s) Humans ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Case-Control Studies ; Nocardia Infections/drug therapy ; Nocardia Infections/etiology ; Nocardia Infections/prevention & control ; Hematopoietic Stem Cell Transplantation/adverse effects ; Risk Factors ; Graft vs Host Disease/prevention & control
    Chemical Substances Trimethoprim, Sulfamethoxazole Drug Combination (8064-90-2)
    Language English
    Publishing date 2022-12-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3062231-1
    ISSN 2666-6367
    ISSN (online) 2666-6367
    DOI 10.1016/j.jtct.2022.12.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5082: Show issues Location:
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  6. Article ; Online: Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis.

    Hong, Hyo-Lim / Flurin, Laure / Thoendel, Matthew J / Wolf, Matthew J / Abdel, Matthew P / Greenwood-Quaintance, Kerryl E / Patel, Robin

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2022  Volume 76, Issue 3, Page(s) e1456–e1462

    Abstract: Background: Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens ... ...

    Abstract Background: Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure.
    Methods: A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq.
    Results: A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83).
    Conclusions: 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.
    MeSH term(s) Humans ; Prosthesis-Related Infections/diagnosis ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Arthritis, Infectious/diagnosis ; Arthroplasty, Replacement, Knee/adverse effects ; Arthroplasty, Replacement, Hip/adverse effects
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2022-08-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/ciac646
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  7. Article ; Online: Toxoplasmosis-Associated Immune Reconstitution Inflammatory Syndrome in an Allogenic Hematopoietic Stem Cell Transplant Recipient.

    Corsini, Cristina / Esquer Garrigos, Zerelda / Welker, Kirk M / Thoendel, Matthew J

    Mayo Clinic proceedings

    2020  Volume 95, Issue 4, Page(s) 823–824

    MeSH term(s) Adult ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Immune Reconstitution Inflammatory Syndrome/complications ; Immune Reconstitution Inflammatory Syndrome/parasitology ; Magnetic Resonance Imaging ; Male ; Neuroimaging ; Toxoplasma ; Toxoplasmosis, Cerebral/diagnosis ; Toxoplasmosis, Cerebral/diagnostic imaging ; Toxoplasmosis, Cerebral/etiology
    Language English
    Publishing date 2020-02-11
    Publishing country England
    Document type Case Reports ; Journal Article
    ZDB-ID 124027-4
    ISSN 1942-5546 ; 0025-6196
    ISSN (online) 1942-5546
    ISSN 0025-6196
    DOI 10.1016/j.mayocp.2020.01.019
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  8. Article: Fusarium

    Chesdachai, Supavit / Almeida, Natalia E Castillo / Comba, Isin Y / Muppa, Prasuna / Thoendel, Matthew J

    IDCases

    2021  Volume 24, Page(s) e01088

    Abstract: Chimeric antigen receptor T-cell (CAR-T) therapy is a novel treatment for various types of hematologic malignancy. We presented a case of refractory diffuse large B cell lymphoma patient who developed acute invasive fungal rhinosinusitis (AIFR) ... ...

    Abstract Chimeric antigen receptor T-cell (CAR-T) therapy is a novel treatment for various types of hematologic malignancy. We presented a case of refractory diffuse large B cell lymphoma patient who developed acute invasive fungal rhinosinusitis (AIFR) from
    Language English
    Publishing date 2021-03-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2745454-X
    ISSN 2214-2509
    ISSN 2214-2509
    DOI 10.1016/j.idcr.2021.e01088
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  9. Article ; Online: Lymphogranuloma Venereum Proctitis.

    Garg, Ishan / Thoendel, Matthew J / Goenka, Ajit H

    Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association

    2017  Volume 15, Issue 8, Page(s) A29–A30

    MeSH term(s) Abdominal Pain/etiology ; Adult ; Gastrointestinal Hemorrhage/microbiology ; Homosexuality, Male ; Humans ; Lymphogranuloma Venereum/diagnosis ; Male ; Proctitis/microbiology ; Rectum
    Language English
    Publishing date 2017-03-29
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 2119789-1
    ISSN 1542-7714 ; 1542-3565
    ISSN (online) 1542-7714
    ISSN 1542-3565
    DOI 10.1016/j.cgh.2017.03.033
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    Zs.A 5836: Show issues Location:
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  10. Article ; Online: Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis.

    Thoendel, Matthew / Jeraldo, Patricio / Greenwood-Quaintance, Kerryl E / Yao, Janet / Chia, Nicholas / Hanssen, Arlen D / Abdel, Matthew P / Patel, Robin

    Journal of clinical microbiology

    2020  Volume 58, Issue 3

    Abstract: Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been ... ...

    Abstract Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All of the tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all of the tools performed well overall, there were some differences, particularly in their predilection for identifying low-abundance or contaminant organisms as present.
    MeSH term(s) Biofilms ; Humans ; Metagenome ; Metagenomics
    Language English
    Publishing date 2020-02-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.00981-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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